
Research Publications
2006 Publication list
Author/s |
Title |
Journal |
Adams, B.J., Bardgett, R.D., Ayres, E., Wall, D.H., Aislabie, J., Bamforth, S., Bargagli, R., Cary, C., Cavacini, P., Connell, L., Convey, P., Fell, J.W., Frati, F., Hogg, I.D., Newsham, K.K., O'Donnell, A., Russell, N., Seppelt, R.D., and Stevens, M.I. | Diversity and Distribution of Victoria Land Biota. | Soil Biology and Biochemistry, 38: 3003-3018. |
Auch, A.F., Henz, S.R., Holland, B.R., and Göker, M. | Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. | BMC Bioinformatics 7:350. |
Barnes, S.S., Matisoo-Smith, E., and Hunt, T. | Ancient DNA of the Pacific Rat (Rattus exulans) from Rapa Nui (Easter Island). | Journal of Archaeological Science 33:1536-1540. |
Baroni, M., Semple, C., and Steel, M. | Hybrids in real time. | Systematic Biology 44(1): 46-56: 2006. |
Baroni, M. and Steel, M. | Accumulation phylogenies. | Annals of Combinatorics 10: 19-30. |
Birchard, G.F., Nelson, N.J., and Daugherty, C.H. | A circadian rhythm in oxygen consumption rate in juvenile tuatara (Sphenodon punctatus). | New Zealand Journal of Zoology 33: 185-188. |
Burnham, D.K., Keall, S.N., Nelson, N.J., and Daugherty, C.H. | Effects of sampling date, gender, and tick burden on peripheral blood cells of captive and wild tuatara (Spendodon punctatus). | New Zealand Journal of Zoology 33: 241-248. |
Chan, C., Ballantyne, K.N., Aikman, H., Chambers, G.K., and Daugherty, C.H | Conservation genetics of the Forbes parakeet (Cyanoramphus forbesi) on Mangere Island, Chatham Islands. | DOC Research & Development Series 254. |
Chan, C., Ballantyne, K.N., Aikman, H., Fastier, D., Chambers, G.K., and Daugherty, C.H. | Genetic analysis of interspecific hybridisation in the world’s only Forbes’ parakeet (Cyanoramphus forbesi) natural population. | Conservation Genetics (7): 493-506. |
Chan, Z., Collins, L. and Kasabov, N. | An efficient greedy K-means algorithm for global gene trajectory clusterin. | Expert Systems with Applications. 30 (1) 137-141. |
Chan, Z.S.H., Kasabov, N. and Collins, L. | A two-stage methodology for gene regulatory network extraction from time-course gene expression data. | Expert Systems with Applications30:59-63. |
Chor, B., Hendy, M.D. and Snir, S. | Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions. | Molecular Biology and Evolution, 23: 626-632. |
Clarke, A.C., Burkenshaw, M., McLenachan, P.A., Erickson, D. and Penny, D. | Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). | Molecular Biology and Evolution 23: 893-900. |
Collins, L.J. and Penny, D. | Investigating the intron recognition mechanism in eukaryotes. | Molecular Biology and Evolution. 23: 901-910. |
Dress, A. and Steel, M. | Mapping edge sets to splits in trees: the path index and parsimony. | Annals of Combinatorics 10: 77-96. |
Donald, K.M. and Spencer, H.G. | Polymorphic microsatellite DNA markers in the mudflat topshell Diloma subrostrata (Gastropoda, Trochidae). | Molecular Ecology Notes (6): 762-764. |
Ewing, G. and Rodrigo, A.G. | Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden. | Evolutionary Bioinformatics Online 2:239-247. |
Gartrell, B.D., Jillings, E., Adlington, B., Mack, H. and Nelson, N.J. | Health screening for a translocation of captive-reared tuatara (Sphenodon punctatus) to an island refuge. | New Zealand Veterinary Journal 54(6): 344-349. |
Gartrell, B., Morgan, K., Owen, M., Hartman, A., Keall, S.N., and Khull, M. | Computed tomographic evaluation of the skulls of three captive tuatara. | Conference Proceedings of the Annual Meeting of the Unusual and Exotic Pets group of the Australian Veterinary Association, pp 41-46. |
Gascuel, O. and Steel, M. | Neighbor-Joining revealed. | Molecular Biology and Evolution23(11): 1997-2000. |
Gernhard, T., Ford, D., Vos, R., and Steel, M. | Estimating the relative order of speciation or coalescence events on a given phylogeny. | Evolutionary Bioinformatics Online 2: 309-317. |
Guindon, S., Black, M., and Rodrigo, A. | Control of the false discovery rate applied to the detection of positively selected amino acid sites. | Mol. Biol. Evol. 23(5):919-926. |
Hare, K.M., Pledger, S., Thompson, M.B., Miller, J.H., and Daugherty, C.H. | Daily patterns of metabolic rate among New Zealand lizards (Reptilia: Lacertilia: Diplodactylidae & Scincidae). | Physiological and Biochemical Zoology 79: 745-753. |
Hartmann, K. and Steel, M. | Maximimizing phylogenetic diversity in biodiverstity conservation: greedy solutions to the Noah's Ark problem. | Systematic Biology 55(4), 644-651. |
Hoare, J.M. and Hare, K.M. | Hoplodactylus maculatus (Common Gecko) toxin consumption. | Herpetological Review 37(1): 86-87. |
Hoare, J.M. and Hare, K.M. | The impact of brodifacoum on non-target wildlife: gaps in knowledge. | New Zealand Journal of Ecology 30(2): 157-167 |
Hoare, J.M. and Nelson, N.J. | Hoplodactylus maculatus (Common Gecko) social assistance. | Herpetological Review 37(2): 222-223. |
Hoare, J.M., Pledger, S., Keall, S.N., Nelson, N.J., Mitchell, N.J. and Daugherty, C.H. | Conservation implications of a long-term decline in body condition in the Brothers Island tuatara, Sphenodon guntheri. | Animal Conservation 9: 456-462. |
Hogg, I.D., Cary, S.C., Convey, P., Newsham, K.K., O'Donnell, A.G., Adams, B.J., Aislabie, J., Frati, F., Stevens, M.I.,Wall, D.H. | Biotic interactions in Antarctic terrestrial ecosystems: are they a factor? | Soil Biology & Biochemistry, 38: 3035-3040. |
Holland, B.R., Jermiin, L.S., and Moulton, V. | Improved consensus network techniques for genome-scale phylogeny. | Molecular Biology and Evolution 23: 848-855. |
Jeffares, D.C., Mourier, T and Penny, D. | The biology of intron gain and loss. | TRENDS in Genetics 22 (1): 16-22. |
Johnson, K.P., Kennedy, M. and McCracken, K.G. | Reinterpreting the Origins of Flamingo Lice: Cospeciation or Host-Switching? | Biology Letters 2: 275-278. |
Kurland, C.G., Collins, L.J., and Penny, D. | Genomics and the Irreducible Nature of Eukaryote Cells. | Science 312: 1011-1014. |
Lambert, D.M. and Millar, C.D. | Large-scale ancient genomics is born! | Nature 444:275-276. |
Lysak, M.A., Berr, A., Pecinka, A., Schmidt, R., McBreen, K. and Schubert, I. | Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. | PNAS 103:5224-5229. |
McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., Scheffer, J., Sims, I., van Heusden, S., Shigyo, M. and Havey, M. J. | Genetic mapping of a major gene affecting onion bulb fructan content. | Theoretical and Applied Genetics 112(5): 958-967. |
McGaughran, A., Hogg, I.D., Stevens, M.I., Chadderton, W.L.and Winterbourn, M.J. | Genetic divergence of three freshwater isopod species from southern New Zealand. | Journal of Biogeography 33: 23-30. |
MacAvoy, E.S., McGibbon, L.M., Sainsbury, J.P., Lawrence, H., Wilson, C.A., Daugherty, C.H. and Chambers, G.K. | Genetic variation in island populations of tuatara (Sphenodon spp.) inferred from microsatellite markers. | Conservation Genetics 8(2): 305-318. |
Matheson, J.W., Rich, F.J., Corbett, C., Greenwood, K., Huang, Q.S., Penny, D., and Hendy, M.D. | Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years. | J Medical Virology 78:1354-1364. |
Meudt, H.M. | A revision of the genus Ourisia (Plantaginaceae). | Systematic Botany Monographs 77: 1-188. |
Meudt, H.M. and Simpson, B.B. | The biogeography of subalpine, austral Ourisia (Plantaginaceae) based on molecular phylogenetic evidence: South American origin and dispersal to New Zealand and Tasmania. | Biological Journal of the Linnean Society 87: 479-513. |
Miller, H.C. | Cloacal and buccal swabs are a reliable source of DNA for microsatellite genotyping of reptiles. | Conservation Genetics 7: 1001-1003. |
Miller, H.C., Belov, K., and Daugherty, C.H. | MHC class I genes in the tuatara (Sphenodon spp.): Evolution of the MHC in an ancient reptilian order. | Molecular Biology and Evolution 23: 949-956. |
Miller, H.C., and Lambert, D.M. | A molecular phylogeny of New Zealand’s Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences. | Molecular Phylogenetics and Evolution 40: 844-855. |
Mitchell, N.J., Nelson, N.J., Cree, A., Pledger, S., Keall, S.N., and Daugherty, C.H. | Support for a rare pattern of temperature-dependent sex determination in archaic reptiles: evidence from two species of tuatara (Sphenodon). | Frontiers in Zoology 3:9. |
Moore, J.A. and Godfrey, S.S. | Sphenodon punctatus (common tuatara). Opportunistic predation. | Herpetological Review 37(1): 81-82. |
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N., and Daugherty, C.H. | Performance of juvenile tuatara depends on age, clutch and incubation regime. | Journal of Herpetology 40(3): 399-403. |
Nielson, M., Lohman, K., Daugherty, C.H., Allendorf, F.W., Knudsen, K.L., and Sullivan, J. | Allozyme and mitochondrial DNA variation in the tailed frog (Anura: Ascaphus): The influence of geography and gene flow. | Herpetologica 62 (3), 235-258. |
Nolan L., Hogg, I.D., Stevens, M.I., and Haase, M. | Fine scale distribution of mtDNA haplotypes for the springtail Gomphiocephalus hodgsoni (Collembola) corresponds to an ancient shoreline in Taylor Valley, continental Antarctica | Polar Biology 29: 813-819. |
Penny, D. | Why the resistance? | EMBO report. Vol 7,no 10: 975. |
Phillips, M.J. | Sympathy for the Devil. | Nature 440. |
Phillips, M.J., McLenachan, P.A., Down, C., Gibb, G.C. and Penny, D. | Combined nuclear and mitochondrial protein -coding DNA sequences resolve the interrelations of the major Australasian marsupial radiations. | Systematic Biology 55: 122-137. |
Poss, M., Ross, H.A., Painter, S.L., Holley, D.C., Terwee, J.A., Vandewoude, S., and Rodrigo, A.G. | Feline lentivirus evolution in cross-species infection reveals high error burdens and selection on key residues in the viral polymerase. | Journal of Virology 80:2728-2737. |
Robins, J.H., Ross, H.A., Allen, M.S., Matisoo-Smith, E.M. | Sus bucculentus revisited. | Nature 440. |
Ross, H.A., Nickle, D.C., Liu. Y., Heath, L., Jensen, M.A., Rodrigo, A.G. and Mullins, J.I. | Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. | Evolutionary Bioinformatics Online 2:18-41. |
Roy, S.W. | Intron rich ancestors. | Trends Genet 22, 468-71. |
Roy, S. W., Ferreira, M. U. and Hartl, D. L. | Evolution of allelic dimorphism in malarial surface antigens. | Heredity [epub online]: 1-8 doi: 10.1038/sj.hdy.6800887. |
Roy, S.W. and Gilbert, W. | The evolution of spliceosomal introns: patterns, puzzles, and progress. | Nat Rev Genet. 7(3): 211-221. |
Roy, S.W., and Hartl, D.L. | Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number. | Genome Research 16 (6): 750-756. |
Roy, S.W., Manuel, I., and Penny, D. | Very Little Intron Gain in Entamoeba histolytica Genes Laterally Transferred from Prokaryotes. | Mol. Biol. Evol. 23(10):1824–1827. |
Roy, S.W., and Penny, D. | Smoke Without Fire: Most Reported Cases of Intron Gain in Nematodes Instead Reflect Intron Losses. | Mol. Biol. Evol. 23(12):2259-2262. |
Sainsbury, J.P., Greene, T.C., Moorhouse, R.J., Daugherty, C.H., and Chambers, G.K. | Microsatellite analysis reveals substantial levels of genetic variation but low levels of genetic divergence among isolated populations of Kaka (Nestor meridionalis). | Emu 106: 329-338. |
Santure, A.W., and Spencer, H.G. | Influence of mom and dad: Quantitative genetic models for maternal effects and imprinting. | Genetics 173: 2297-2316. |
Semple, C. and Steel, M. | Unicyclic networks: compatibility and enumeration.IEEE/ACM | Transactions on Computational Biology and Bioinformatics 3(1), 84-91. |
Shepherd, L.D. and Lambert, D.M. | Nuclear microsatellite DNA markers for New Zealand kiwi (Apteryx spp.). | Molecular Ecology Notes 6: 227-229. |
Sinclair, B.J., and Stevens, M.I. | Terrestrial microarthropods of Victoria Land and Queen Maud Mountains, Antarctica: implications of climate change. | Soil Biology & Biochemistry, 38: 3158-3170 . |
Slack, K.E., Jones, C.M., Ando, T., Harrison, G.L., Fordyce, E., Arnason, U. and Penny, D. | Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. | Molecular Biology and Evolution 23: 1144-1155. |
Spencer, H.G. | Evolution of genomic imprinting in mammals. | In Encyclopedia of Genomics, Proteomics and Bioinformatics, M. Dunn, L. Jorde, P. Little and S. Subramaniam (eds). John Wiley, Chichester, UK |
Spencer, H.G., Brook, F.J. and Kennedy, M. | Phylogeography of Kauri Snails and their Allies from Northland, New Zealand (Mollusca: Gastropoda: Rhytididae: Paryphantinae). | Molecular Phylogenetics and Evolution 38: 835-842. |
Spencer, H.G., and Clark, A.G. | A chip off the old block: A model for the evolution of genomic imprinting via selection for parental similarity. | Genetics 174: 931-935 |
Spencer, H.G., Dorn, T., and LoFaro, T. | Population models of genomic imprinting. II. Maternal and fertility selection. | Genetics 173:2391-2398. |
Steel, M. and Hein, J. | Reconstructing pedigrees: a combinatorial perspective. | Journal of Theoretical Biology 240(3): 360-367. |
Steel, M. and Pickett, K.M. | On the impossibility of uniform priors on clade size. | Molecular Phylogenetics and Evolution 39(2): 585-586. |
Steel, M. and Szekely, L. | On the variational distance of two trees, | Annals of Applied Probability 16(3): 1563-1575. |
Stevens, M.I., Fjellberg, A., Greenslade, P., Hogg, I.D., and Sunnucks, P. | Redescription of the Antarctic springtail Desoria klovstadi using morphological and molecular evidence. | Polar Biology, 29: 820-830 . |
Stevens, M.I., Greenslade, P., Hogg, I.D. and Sunnucks, P. | Examining Southern Hemisphere springtails: could any have survived glaciation of Antarctica? | Molecular Biology and Evolution 23: 874-882. |
Stevens, M.I., and Hogg, I.D. | Contrasting levels of mitochondrial DNA variability between mites (Penthalodidae) and springtails (Hypogastruridae) from the Trans-Antarctic Mountains suggest long-term effects of glaciation and life history on substitution rates, and speciation processes. | Soil Biology & Biochemistry, 38: 3171-3180 . |
Stevens, M.I., Hogg, I.D. and Pilditch, C.A. | Evidence for female-biased juvenile dispersal in corophiid amphipods from a New Zealand estuary. | Journal of Experimental Marine Biology and Ecology 331: 9-20. |
Thatte, B.D. | Invertibility of the TKF model of sequence evolution. | Mathematical Biosciences 200,(1): 58-75. |
Towns, D.R., Atkinson, I.A.E., and Daugherty, C.H. | Have the harmful effects of introduced rats on islands been exaggerated? | Biological Invasions 8(4): 863-891 |
Woodhams, M. | Can Deleterious Mutations Explain the Time Dependency of Molecular Rate Estimates? | Mol. Biol. Evol., 23(12):2271-2273. |
Zauner, S., Lockhart, P.J., Stoebe-Maier, B., Gilson, P., McFadden, G.I. and Maier, U.G. | Differential Gene Transfers and Gene Duplications in Primary and Secondary Endosymbioses. | BioMed Central 6: 38. |